October 25, 2012

This seems like an interesting theory that might explain two facts that do not appear to gel well with existing models of a single (or few) short and intense periods of admixture during Out-of-Africa. These are:

The complete absence of archaic Eurasian Y chromosomes and mtDNA in the modern human gene pool

The fact that Neandertals did not appear to have gotten morphologically more different than modern humans over most of their late history, but rather the opposite, they became ever-more similar to modern humans

It would also have three added benefits:

it would be a very natural consequence of my favored scenario that modern humans (living probably in northern and eastern Africa) had Neandertal neighbors living in the Near East and southern Europe from which they were separated by geographical barriers, making admixture likely but not routine. The authors consider the idea that the admixture took place in the Near East, and even if some of it did not, I'd say most of it must have taken place there, since that is where maximal evidence of temporal co-existence between the two demes exists.

it would not require an unlikely scenario of large-scale hybridization between very divergent demes: occasional gene flow could still occur, and could spread adaptations back and forth (explaining the phenotypic non-divergence), but the tendency of people to marry those like themselves (homogamy) would be preserved.

It would be consistent with the re-writing of Out-of-Africa thanks to the halving of the autosomal rate. This would necessitate an early OoA and thus a longer occupation of parts of Asia by both sapiens and Neandertals.during which they may have occasionally interbred. So, not only were modern humans and Neandertals neighbors in Asia, but modern Eurasians are not descended from a fresh ~50ka Out-of-Sub-Saharan Africa expansion that would have rendered these long neighborly relations in the Near East irrelevant.

Note that this does not appear to be inconsistent with recent dating of the modern human-Neandertal admixture by Sankararaman et al. since that involved only the latest period of admixture. It is also not inconsistent with the idea that archaic African admixture may be contributing to the D-statistic evidence for non-African/Neandertal similarity, since, presumably, modern humans could experience low-level gene flow both with their northern Neandertal neighbors, and their southern archaic African ones.

So, all in all, I'm fairly sympathetic to this model, and I'd be interested to see how it is received by experts in this field.

Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to 4% of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.

Neanderthals and humans were not that physically dissimilar after all. For example, a human male with no sexual outlet within human females could easily disregard inhibitions and copulate with a neanderthal female (and vice versa). The degree of difference between neanderthals and humans was for sure much smaller than the inter-species degree of difference documented in present day examples of human bestiality. Of course, the fertility of these matings is an entirely different issue.

it would not require an unlikely scenario of large-scale hybridization between very divergent demes: occasional gene flow could still occur

Here is exactly the flaw in this investigation. Occasional gene flow between very divergent demes would be unable to phase out a clear hybridization signal. For instance, Denisovans and their descendants show such a signal in chromosome 11, and Denisovan segments of chr X are missing altogether in modern populations. The rather equal distribution of Neanderthal admixtures over all autosomes should thus be either indicative of a much more frequent contact, or - more interesting - a very close genetic relation of Neanderthal, that vastly exceed the genetic distance with Denisovans. The latter, by the way, was so far not really substantiated.

I can't see how this theory explains the lack of uni-parental genetic heritage. Long running rare admixture does not decrease the probability of uni-parental genetic contribution compared to a short time frequent interbreeding in any obvious way, as far as the overall genetic impact is about the same.

Also one interbreeding in every 77 generation possibly can explain the Neanderthal genetic impact in the modern population, but I think for the whole Neanderthal population to converge to the modern humans, we need more than that. You suggested a significant convergence in your earlier posts.

At the moment I see three possible explanations for the lack of Neanderthal uni-parental genes in the current population (other than blind chance). 1. The reference Neanderthal Vindija sample is already strongly interbreed, so most of the aDNA signal is false.2. The admixture was very low level, but some of the Nenderthal alleles were under strong positive selection in some time. 3. The Neanderthal mDNA and yDNA were under strong negative selection (while most of the autosomal alleles were not).

Long running rare admixture does not decrease the probability of uni-parental genetic contribution compared to a short time frequent interbreeding in any obvious way, as far as the overall genetic impact is about the same.

The probability of loss of a new mutation depends on the initial frequency.

You can think of it as follows: if you start with 100 introgressed alleles in the population, then the # alleles starts executing a random walk, going up and down from the initial 100, and only rarely gets down to 0 which is non-recoverable.

On the other hand, if you introduce 1 new allele, then with a good probability you go down to zero right away, or in a few steps, which is "non-recoverable", i.e., the frequency gets stuck in zero.

"The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome".

Makes sense to me.

"I can't see how this theory explains the lack of uni-parental genetic heritage. Long running rare admixture does not decrease the probability of uni-parental genetic contribution compared to a short time frequent interbreeding in any obvious way, as far as the overall genetic impact is about the same".

At each admixture occasion Neanderthal haplogroups would make up a minority of the 'modern human' population. At small population numbers minority haplogroups would be drifted out.

"Also one interbreeding in every 77 generation possibly can explain the Neanderthal genetic impact in the modern population"

But remember that those neanderthals had adapted to the Northern Eurasia eco-region for thousands of years. We would expect some of their genes to help modern humans survive in it too. Seklection for those genes would operate.

The % of admixture isn't as interesting as the range of the admixed genes. A single, or a few events very early on could result in what we see, as far as the % admixture. If there were many separate admix events, then with each event different genes would be passed on, resulting in, I would think, a much wider variety in the Neanderthal genes being passed on.Somewhere I read that while East Asians have similar % admix, the genes represented are not the same genes as seen in Europeans. If so that suggests to me that there were separate admix events.

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